After the 8.1 update mine gives me the same warning, I also get the warning with the touch cover. I have noticed some problems with both touch and type covers when typing in the search box and when trying to log in to my email, hopefully they will correct it ASAP

Try to uninstall the "Surface Touch Cover Firmware" driver. Make sure to also check "Delete the driver software for this device" as well.
Once done, just press the "Scan for hardware changes" button and it will re-add the driver automatically.
The error should be gone now.